First pass at a Hanging Protocol implementation and editor (LT-131)

This commit is contained in:
Erik Ziegler committed 2016-05-07 12:40:02 +02:00
1 parent dfcb33153f
commit 2e52d9e3c1
157 files changed
+8869 -23585

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@@ -0,0 +1,17 @@
<template name="progressDialog">
<div id="progressDialog" tabindex="0">
<div class="dialogHeader">
<h5>{{progressDialogTitle}}</h5>
</div>
<div class="dialogContent">
<div class="progress">
<div class="progress-bar progress-bar-striped active" role="progressbar" style="width:{{progressStatus}}">
{{progressStatus}}
</div>
</div>
<div id="message">
{{{progressMessage}}}
</div>
</div>
</div>
</template>
@@ -0,0 +1,56 @@
progressDialog = {
'show': function(title, numberOfTotal) {
Session.set("progressDialogSettings", { title: title, numberOfCompleted: 0, numberOfTotal: numberOfTotal });
$('#progressDialog').css('display', 'block');
},
'update': function(numberOfCompleted) {
var progressDialogSettings = Session.get("progressDialogSettings");
progressDialogSettings.numberOfCompleted = numberOfCompleted;
Session.set("progressDialogSettings", progressDialogSettings);
if (progressDialogSettings.numberOfCompleted === progressDialogSettings.numberOfTotal) {
progressDialog.close();
}
},
'close': function() {
Session.set("progressDialogSettings", { title: "", numberOfCompleted: 0, numberOfTotal: 1 });
$('#progressDialog').css('display', 'none');
},
'setMessage': function(message) {
var progressDialogSettings = Session.get("progressDialogSettings");
progressDialogSettings.message = message;
Session.set("progressDialogSettings", progressDialogSettings);
}
};
Template.progressDialog.helpers({
'progressDialogTitle': function () {
if (Session.get("progressDialogSettings") && Session.get("progressDialogSettings").title) {
return Session.get("progressDialogSettings").title;
}
return "";
},
'progressStatus': function() {
var numberOfCompleted = 0;
if (Session.get("progressDialogSettings") && Session.get("progressDialogSettings").numberOfCompleted) {
numberOfCompleted = Session.get("progressDialogSettings").numberOfCompleted;
}
var numberofTotal = 1;
if (Session.get("progressDialogSettings") && Session.get("progressDialogSettings").numberOfTotal) {
numberofTotal = Session.get("progressDialogSettings").numberOfTotal;
}
return parseInt((numberOfCompleted / numberofTotal) * 100) + "%";
},
'progressMessage': function() {
var progressDialogSettings = Session.get("progressDialogSettings");
if (progressDialogSettings && progressDialogSettings.message) {
return progressDialogSettings.message;
}
return;
}
});
@@ -0,0 +1,25 @@
#progressDialog
display: none
position: absolute
top: 0
bottom: 0
left: 0
right: 0
margin: auto
width: 20%
height: 20%
z-index: 100
border-radius: 5px
padding: 10px 20px 10px 20px
background-color: rgba(255,255,255,1)
outline: none
.dialogContent
margin-bottom: 20px
#message
width: 100%
span
display: inline-block;
width: 100%
@@ -20,10 +20,20 @@ WorklistStudies = new Meteor.Collection(null);
WorklistStudies._debugName = 'WorklistStudies';
Template.worklist.onRendered(function() {
// If there is a tab set as active in the Session,
// switch to that now.
var contentId = Session.get('activeContentId');
switchToTab(contentId);
var templateData = Template.currentData();
if (templateData && templateData.studyInstanceUid) {
var studyInstanceUid = templateData.studyInstanceUid;
openNewTab(studyInstanceUid, studyInstanceUid);
} else {
// If there is a tab set as active in the Session,
// switch to that now.
var contentId = Session.get('activeContentId');
// TODO: FIx this it seems to be forcing two switches
switchToTab(contentId);
}
Meteor.subscribe('hangingprotocols');
});
Template.worklist.helpers({
@@ -97,5 +97,4 @@
{{>studyNotFound}}
{{/if}}
</div>
</template>
@@ -164,7 +164,7 @@ function search() {
});
if (WorklistStudies.find().count() === 0) {
// Show notFound text
// Show studyNotFound text
searchResults.showNotFoundMessage = true;
Session.set('searchResults', searchResults);
}
@@ -104,4 +104,4 @@
border-top: 0.5px dashed #dddddd
border-bottom: 0.5px dashed #dddddd
color: white
background-color: #009BD2
background-color: #009BD2
@@ -0,0 +1,115 @@
var exportFailed;
/**
* Exports requested studies
* @param studiesToExport Studies to export
*/
exportStudies = function(studiesToExport) {
if (studiesToExport.length < 1) {
return;
}
queryStudies(studiesToExport, exportQueriedStudies);
};
function exportQueriedStudies(studiesToExport) {
var numberOfFilesToExport = 0;
studiesToExport.forEach(function(study) {
numberOfFilesToExport += getNumberOfFilesInStudy(study);
});
progressDialog.show("Exporting Studies...", numberOfFilesToExport);
try {
exportQueriedStudiesInternal(studiesToExport, numberOfFilesToExport);
} catch (err) {
progressDialog.close();
console.error("Failed to export studies: " + err.message);
}
}
function exportQueriedStudiesInternal(studiesToExport, numberOfFilesToExport) {
var zip = new JSZip();
exportFailed = false;
var numberOfFilesExported = 0;
studiesToExport.forEach(function(study) {
sortStudy(study);
var studyFolder = zip.folder(study.studyInstanceUid);
study.seriesList.forEach(function(series) {
var seriesFolder = studyFolder.folder(series.seriesInstanceUid);
series.instances.forEach(function(instance) {
if (!instance.wadouri) {
return;
}
// If failed to download a dicom file, skip others
if (exportFailed) {
return;
}
// Download and Zip the dicom file
var xhr = new XMLHttpRequest();
xhr.open("GET", instance.wadouri, true);
xhr.responseType = "blob";
// Downloaded the dicom file completely
xhr.onload = function(e) {
// If failed to download a dicom file, skip others
if (exportFailed) {
return;
}
// Failed to export a file
if (xhr.readyState === 4 && xhr.status !== 200) {
onExportFailed("File not downloaded: " + instance.wadouri);
return;
}
var blobFile = new Blob([xhr.response], {type: 'application/dicom'});
var fileReader = new FileReader();
fileReader.onload = function() {
try {
seriesFolder.file(instance.sopInstanceUid + ".dcm", fileReader.result, { binary: true });
} catch(err) {
onExportFailed(err.message);
return;
}
numberOfFilesExported++;
if (numberOfFilesExported === numberOfFilesToExport) {
var zipContent = zip.generate({ type: "blob" });
saveAs(zipContent, "studies.zip");
}
progressDialog.update(numberOfFilesExported);
};
fileReader.readAsArrayBuffer(blobFile);
};
// Failed to download the dicom file
xhr.onerror = function() {
onExportFailed("File not downloaded: " + instance.wadouri);
};
xhr.send();
});
});
});
}
function onExportFailed(err) {
exportFailed = true;
progressDialog.close();
//TODO: Export failed and dialog closed, so let user know
console.error("Failed to export studies!", err);
}
@@ -22,10 +22,6 @@ getStudiesMetadata = function(studyInstanceUids, doneCallback, failCallback) {
// retrieval call
var promises = [];
// Create an empty array to hold all the results of the promises
var studies = [];
// Loop through the array of studyInstanceUids
studyInstanceUids.forEach(function(studyInstanceUid) {
// Create a new Deferred to monitor the progress of the asynchronous
@@ -24,12 +24,12 @@ getStudyMetadata = function(studyInstanceUid, doneCallback, failCallback) {
// If no study metadata is in the cache variable, we need to retrieve it from
// the server with a call.
Meteor.call('GetStudyMetadata', studyInstanceUid, function(error, study) {
if (Meteor.user()) {
if (Meteor.user && Meteor.user()) {
var hipaaEvent = {
eventType: "viewed",
eventType: 'viewed',
userId: Meteor.userId(),
userName: Meteor.user().profile.fullName,
collectionName: "Study",
collectionName: 'Study',
recordId: studyInstanceUid,
patientId: study.patientId,
patientName: study.patientName
@@ -55,4 +55,4 @@ getStudyMetadata = function(studyInstanceUid, doneCallback, failCallback) {
// Finally, we fire the doneCallback with this study meta data
doneCallback(study);
});
};
};
@@ -15,6 +15,7 @@ openNewTab = function(studyInstanceUid, title) {
WorklistTabs.insert({
title: title,
contentid: contentid,
studyInstanceUid: studyInstanceUid,
active: false
});
File renamed without changes.
+39 -8
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@@ -5,7 +5,7 @@ Package.describe({
});
Package.onUse(function (api) {
api.versionsFrom('1.2.0.2');
api.versionsFrom('1.2.1');
api.use('standard-app-packages');
api.use('jquery');
@@ -17,11 +17,13 @@ Package.onUse(function (api) {
// Our custom packages
api.use('dicomweb');
api.use('dimseservice');
api.use('orthanc-remote');
// This sets the default logging level of the package using the
// loglevel package. It can be overridden in the JavaScript
// console for debugging purposes
api.addFiles('log.js', 'client');
api.addFiles('log.js');
// Components
api.addFiles('client/components/worklist.html', 'client');
@@ -51,12 +53,40 @@ Package.onUse(function (api) {
api.addFiles('client/components/worklistToolbar/worklistToolbar.js', 'client');
api.addFiles('client/components/worklistToolbar/worklistToolbar.styl', 'client');
// Library functions
api.addFiles('lib/getStudyMetadata.js', 'client');
api.addFiles('lib/getStudiesMetadata.js', 'client');
api.addFiles('lib/openNewTab.js', 'client');
api.addFiles('lib/switchToTab.js', 'client');
api.addFiles('lib/worklist.js', 'client');
api.addFiles('client/components/progressDialog/progressDialog.html', 'client');
api.addFiles('client/components/progressDialog/progressDialog.styl', 'client');
api.addFiles('client/components/progressDialog/progressDialog.js', 'client');
// Client-side library functions
api.addFiles('client/lib/getStudyMetadata.js', 'client');
api.addFiles('client/lib/getStudiesMetadata.js', 'client');
api.addFiles('client/lib/openNewTab.js', 'client');
api.addFiles('client/lib/switchToTab.js', 'client');
api.addFiles('client/lib/exportStudies.js', 'client');
api.addFiles('client/lib/worklist.js', 'client');
// Server-side functions
api.addFiles('server/lib/namespace.js', 'server');
api.addFiles('server/lib/encodeQueryData.js', 'server');
api.addFiles('server/methods/getStudyMetadata.js', 'server');
api.addFiles('server/methods/worklistSearch.js', 'server');
// DICOMWeb instance, study, and metadata retrieval
api.addFiles('server/services/qido/instances.js', 'server');
api.addFiles('server/services/qido/studies.js', 'server');
api.addFiles('server/services/wado/retrieveMetadata.js', 'server');
// DIMSE instance, study, and metadata retrieval
api.addFiles('server/services/dimse/instances.js', 'server');
api.addFiles('server/services/dimse/studies.js', 'server');
api.addFiles('server/services/dimse/retrieveMetadata.js', 'server');
// Study, instance, and metadata retrieval from remote PACS via Orthanc as a proxy
api.addFiles('server/services/remote/instances.js', 'server');
api.addFiles('server/services/remote/studies.js', 'server');
api.addFiles('server/services/remote/retrieveMetadata.js', 'server');
api.export('Services', 'server');
// Export Worklist helper functions for usage in Routes
api.export('getTimepointName', 'client');
@@ -65,6 +95,7 @@ Package.onUse(function (api) {
api.export('openNewTab', 'client');
api.export('setWorklistSubscriptions', 'client');
api.export('switchToTab', 'client');
api.export('progressDialog', 'client');
api.export('Worklist');
// Export the global ViewerData object
@@ -0,0 +1,18 @@
/**
* Converts the properties to URL query parameters. Based on:
* http://stackoverflow.com/questions/111529/create-query-parameters-in-javascript
*
* @param data
* @returns {string}
*/
encodeQueryData = function(data) {
var ret = [];
for (var d in data) {
if (data[d]) {
ret.push(encodeURIComponent(d) + '=' + encodeURIComponent(data[d]));
}
}
return ret.join('&');
};
@@ -0,0 +1,9 @@
Services = {};
Services.QIDO = {};
Services.WADO = {};
Services.DIMSE = {};
Services.REMOTE = {};
remoteGetValue = function(obj) {
return obj ? obj.Value : null;
};
@@ -0,0 +1,22 @@
Meteor.methods({
/**
* Retrieves Study metadata given a Study Instance UID
* This Meteor method is available from both the client and the server
*/
GetStudyMetadata: function(studyInstanceUid) {
log.info('GetStudyMetadata(%s)', studyInstanceUid);
if (!Meteor.settings.dicomWeb) {
throw 'No properly configured server was available over DICOMWeb';
}
if (Meteor.settings.dicomWeb && Meteor.settings.defaultServiceType === 'dicomWeb') {
// Get the server data. This is user-defined in the
// config.json files used to run the Meteor server
var server = Meteor.settings.dicomWeb.endpoints[0];
return Services.WADO.RetrieveMetadata(server, studyInstanceUid);
} else if (Meteor.settings.dimse && Meteor.settings.defaultServiceType === 'dimse') {
return Services.DIMSE.RetrieveMetadata(studyInstanceUid);
}
}
});
@@ -0,0 +1,19 @@
Meteor.methods({
/**
* Use the specified filter to conduct a search from the DICOM server
* @param filter
*/
WorklistSearch: function(filter) {
if (Meteor.settings.dicomWeb && Meteor.settings.defaultServiceType === 'dicomWeb') {
// Get the server data. This is user-defined in the
// config.json files used to run the Meteor server
var server = Meteor.settings.dicomWeb.endpoints[0];
return Services.QIDO.Studies(server, filter);
} else if (Meteor.settings.dimse && Meteor.settings.defaultServiceType === 'dimse') {
return Services.DIMSE.Studies(filter);
} else {
throw 'No properly configured server was available over DICOMWeb or DIMSE.';
}
}
});
+66
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@@ -0,0 +1,66 @@
/**
* Parses data returned from a study search and transforms it into
* an array of series that are present in the study
*
* @param resultData
* @returns {Array} Series List
*/
function resultDataToStudyMetadata(resultData) {
var seriesMap = {};
var seriesList = [];
resultData.forEach(function(instanceRaw) {
var instance = instanceRaw.toObject();
// Use seriesMap to cache series data
// If the series instance UID has already been used to
// process series data, continue using that series
var seriesInstanceUid = instance[0x0020000E];
var series = seriesMap[seriesInstanceUid];
// If no series data exists in the seriesMap cache variable,
// process any available series data
if (!series) {
series = {
seriesInstanceUid: seriesInstanceUid,
seriesNumber: instance[0x00200011],
instances: []
};
// Save this data in the seriesMap cache variable
seriesMap[seriesInstanceUid] = series;
seriesList.push(series);
}
var host = Meteor.settings.dimse.host,
port = Meteor.settings.dimse.port;
var serverRoot = host + ':' + port;
var sopInstanceUid = instance[0x00080018];
var uri = serverRoot + '/studies/' + studyInstanceUid + '/series/' + seriesInstanceUid + '/instances/' + sopInstanceUid + '/frames/1';
// Add this instance to the current series
series.instances.push({
sopClassUid: instance[0x00080016],
sopInstanceUid: sopInstanceUid,
uri: uri,
instanceNumber: instance[0x00200013]
});
});
return seriesList;
}
/**
* Retrieve a set of instances using a DIMSE call
* @param studyInstanceUid
* @returns {{wadoUriRoot: String, studyInstanceUid: String, seriesList: Array}}
*/
Services.DIMSE.Instances = function(studyInstanceUid) {
//var url = buildUrl(server, studyInstanceUid);
var result = DIMSE.retrieveInstances(studyInstanceUid);
return {
studyInstanceUid: studyInstanceUid,
seriesList: resultDataToStudyMetadata(result)
};
};
+125
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@@ -0,0 +1,125 @@
/**
* Parses the SourceImageSequence, if it exists, in order
* to return a ReferenceSOPInstanceUID. The ReferenceSOPInstanceUID
* is used to refer to this image in any accompanying DICOM-SR documents.
*
* @param instance
* @returns {String} The ReferenceSOPInstanceUID
*/
function getSourceImageInstanceUid(instance) {
// TODO= Parse the whole Source Image Sequence
// This is a really poor workaround for now.
// Later we should probably parse the whole sequence.
var SourceImageSequence = instance[0x00082112];
if (SourceImageSequence && SourceImageSequence.length) {
return SourceImageSequence[0][0x00081155];
}
}
/**
* Parses result data from a DIMSE search into Study MetaData
* Returns an object populated with study metadata, including the
* series list.
*
* @param resultData
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
*/
function resultDataToStudyMetadata(studyInstanceUid, resultData) {
log.info('resultDataToStudyMetadata');
var seriesMap = {};
var seriesList = [];
if (!resultData.length) {
return;
}
var anInstance = resultData[0].toObject();
if (!anInstance) {
return;
}
var studyData = {
seriesList: seriesList,
patientName: anInstance[0x00100010],
patientId: anInstance[0x00100020],
accessionNumber: anInstance[0x00080050],
studyDate: anInstance[0x00080020],
modalities: anInstance[0x00080061],
studyDescription: anInstance[0x00081030],
imageCount: anInstance[0x00201208],
studyInstanceUid: anInstance[0x0020000D]
};
resultData.forEach(function(instanceRaw) {
var instance = instanceRaw.toObject();
var seriesInstanceUid = instance[0x0020000E];
var series = seriesMap[seriesInstanceUid];
if (!series) {
series = {
seriesDescription: instance[0x0008103E],
modality: instance[0x00080060],
seriesInstanceUid: seriesInstanceUid,
seriesNumber: parseFloat(instance[0x00200011]),
instances: []
};
seriesMap[seriesInstanceUid] = series;
seriesList.push(series);
}
var sopInstanceUid = instance[0x00080018];
var instanceSummary = {
imageType: instance[0x00080008],
sopClassUid: instance[0x00080016],
sopInstanceUid: sopInstanceUid,
instanceNumber: parseFloat(instance[0x00200013]),
imagePositionPatient: instance[0x00200032],
imageOrientationPatient: instance[0x00200037],
frameOfReferenceUID: instance[0x00200052],
sliceLocation: parseFloat(instance[0x00201041]),
samplesPerPixel: parseFloat(instance[0x00280002]),
photometricInterpretation: instance[0x00280004],
rows: parseFloat(instance[0x00280010]),
columns: parseFloat(instance[0x00280011]),
pixelSpacing: instance[0x00280030],
bitsAllocated: parseFloat(instance[0x00280100]),
bitsStored: parseFloat(instance[0x00280101]),
highBit: parseFloat(instance[0x00280102]),
pixelRepresentation: parseFloat(instance[0x00280103]),
windowCenter: instance[0x00281050],
windowWidth: instance[0x00281051],
rescaleIntercept: parseFloat(instance[0x00281052]),
rescaleSlope: parseFloat(instance[0x00281053]),
sourceImageInstanceUid: getSourceImageInstanceUid(instance),
laterality: instance[0x00200062],
viewPosition: instance[0x00185101],
numFrames: parseFloat(instance[0x00280008]),
frameTime: parseFloat(instance[0x00181063])
};
// Retrieve the actual data over WADO-URI
var server = Meteor.settings.dicomWeb.endpoints[0];
instanceSummary.wadouri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + "&contentType=application%2Fdicom";
series.instances.push(instanceSummary);
});
return studyData;
}
/**
* Retrieved Study MetaData from a DICOM server using DIMSE
* @param studyInstanceUid
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
*/
Services.DIMSE.RetrieveMetadata = function(studyInstanceUid) {
var result = DIMSE.retrieveInstances(studyInstanceUid);
var study = resultDataToStudyMetadata(studyInstanceUid, result);
if (!study) {
study = {};
}
study.studyInstanceUid = studyInstanceUid;
return study;
};
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@@ -0,0 +1,47 @@
/**
* Parses resulting data from a QIDO call into a set of Study MetaData
*
* @param resultData
* @returns {Array} An array of Study MetaData objects
*/
function resultDataToStudies(resultData) {
var studies = [];
resultData.forEach(function(studyRaw) {
var study = studyRaw.toObject();
studies.push({
studyInstanceUid: study[0x0020000D],
// 00080005 = SpecificCharacterSet
studyDate: study[0x00080020],
studyTime: study[0x00080030],
accessionNumber: study[0x00080050],
referringPhysicianName: study[0x00080090],
// 00081190 = URL
patientName: study[0x00100010],
patientId: study[0x00100020],
patientBirthdate: study[0x00100030],
patientSex: study[0x00100040],
imageCount: study[0x00201208],
studyId: study[0x00200010],
studyDescription: study[0x00081030],
modalities: study[0x00080061]
});
});
return studies;
}
Services.DIMSE.Studies = function(filter) {
log.info('Services.DIMSE.Studies');
var parameters = {
0x00100010: filter.patientName,
0x00100020: filter.patientId,
0x00080050: filter.accessionNumber,
0x00081030: filter.studyDescription,
0x00100040: '',
0x00201208: '',
0x00080061: ''
};
var results = DIMSE.retrieveStudies(parameters);
return resultDataToStudies(results);
};
@@ -0,0 +1,83 @@
/**
* Creates a QIDO URL given the server settings and a study instance UID
* @param server
* @param studyInstanceUid
* @returns {string} URL to be used for QIDO calls
*/
function buildUrl(server, studyInstanceUid) {
return server.qidoRoot + '/studies/' + studyInstanceUid + '/instances';
}
/**
* Parses data returned from a QIDO search and transforms it into
* an array of series that are present in the study
*
* @param server The DICOM server
* @param studyInstanceUid
* @param resultData
* @returns {Array} Series List
*/
function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
var seriesMap = {};
var seriesList = [];
resultData.forEach(function(instance) {
// Use seriesMap to cache series data
// If the series instance UID has already been used to
// process series data, continue using that series
var seriesInstanceUid = DICOMWeb.getString(instance['0020000E']);
var series = seriesMap[seriesInstanceUid];
// If no series data exists in the seriesMap cache variable,
// process any available series data
if (!series) {
series = {
seriesInstanceUid: seriesInstanceUid,
seriesNumber: DICOMWeb.getString(instance['00200011']),
instances: []
};
// Save this data in the seriesMap cache variable
seriesMap[seriesInstanceUid] = series;
seriesList.push(series);
}
// The uri for the dicomweb
// NOTE: DCM4CHEE seems to return the data zipped
// NOTE: Orthanc returns the data with multi-part mime which cornerstoneWADOImageLoader doesn't
// know how to parse yet
//var uri = DICOMWeb.getString(instance['00081190']);
//uri = uri.replace('wado-rs', 'dicom-web');
// manually create a WADO-URI from the UIDs
// NOTE: Haven't been able to get Orthanc's WADO-URI to work yet - maybe its not configured?
var sopInstanceUid = DICOMWeb.getString(instance['00080018']);
var uri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + '&contentType=application%2Fdicom';
// Add this instance to the current series
series.instances.push({
sopClassUid: DICOMWeb.getString(instance['00080016']),
sopInstanceUid: sopInstanceUid,
uri: uri,
instanceNumber: DICOMWeb.getString(instance['00200013'])
});
});
return seriesList;
}
/**
* Retrieve a set of instances using a QIDO call
* @param server
* @param studyInstanceUid
* @returns {{wadoUriRoot: String, studyInstanceUid: String, seriesList: Array}}
*/
Services.QIDO.Instances = function(server, studyInstanceUid) {
var url = buildUrl(server, studyInstanceUid);
var result = DICOMWeb.getJSON(url, server.requestOptions);
return {
wadoUriRoot: server.wadoUriRoot,
studyInstanceUid: studyInstanceUid,
seriesList: resultDataToStudyMetadata(server, studyInstanceUid, result.data)
};
};
@@ -0,0 +1,65 @@
/**
* Produces a QIDO URL given server details and a set of specified search filter
* items
*
* @param server
* @param filter
* @returns {string} The URL with encoded filter query data
*/
function filterToQIDOURL(server, filter) {
var commaSeparatedFields = [
'00081030', // Study Description
'00080060' //Modality
// Add more fields here if you want them in the Study List
].join(',');
var parameters = {
PatientName: filter.patientName,
PatientID: filter.patientId,
AccessionNumber: filter.accessionNumber,
StudyDescription: filter.studyDescription,
limit: filter.limit || 20,
includefield: server.qidoSupportsIncludeField ? 'all' : commaSeparatedFields
};
return server.qidoRoot + '/studies?' + encodeQueryData(parameters);
}
/**
* Parses resulting data from a QIDO call into a set of Study MetaData
*
* @param resultData
* @returns {Array} An array of Study MetaData objects
*/
function resultDataToStudies(resultData) {
var studies = [];
resultData.forEach(function(study) {
studies.push({
studyInstanceUid: DICOMWeb.getString(study['0020000D']),
// 00080005 = SpecificCharacterSet
studyDate: DICOMWeb.getString(study['00080020']),
studyTime: DICOMWeb.getString(study['00080030']),
accessionNumber: DICOMWeb.getNumber(study['00080050']),
referringPhysicianName: DICOMWeb.getString(study['00080090']),
// 00081190 = URL
patientName: DICOMWeb.getName(study['00100010']),
patientId: DICOMWeb.getString(study['00100020']),
patientBirthdate: DICOMWeb.getString(study['00100030']),
patientSex: DICOMWeb.getString(study['00100040']),
studyId: DICOMWeb.getString(study['00200010']),
numberOfStudyRelatedSeries: DICOMWeb.getString(study['00201206']),
numberOfStudyRelatedInstances: DICOMWeb.getString(study['00201208']),
studyDescription: DICOMWeb.getString(study['00081030']),
// modality: DICOMWeb.getString(study['00080060']),
// modalitiesInStudy: DICOMWeb.getString(study['00080061']),
modalities: DICOMWeb.getString(DICOMWeb.getModalities(study['00080060'], study['00080061']))
});
});
return studies;
}
Services.QIDO.Studies = function(server, filter) {
var url = filterToQIDOURL(server, filter);
var result = DICOMWeb.getJSON(url, server.requestOptions);
return resultDataToStudies(result.data);
};
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/**
* Parses data returned from a QIDO search and transforms it into
* an array of series that are present in the study
*
* @param server The DICOM server
* @param studyInstanceUid
* @param resultData
* @returns {Array} Series List
*/
function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
var seriesMap = {};
var seriesList = [];
resultData.forEach(function(instance) {
// Use seriesMap to cache series data
// If the series instance UID has already been used to
// process series data, continue using that series
var seriesInstanceUid = remoteGetValue(instance['0020,000e']);
var series = seriesMap[seriesInstanceUid];
// If no series data exists in the seriesMap cache variable,
// process any available series data
if(!series) {
series = {
seriesInstanceUid : seriesInstanceUid,
seriesNumber : parseFloat(remoteGetValue(instance['0020,0011'])),
instances: []
};
// Save this data in the seriesMap cache variable
seriesMap[seriesInstanceUid] = series;
seriesList.push(series);
}
// The uri for the dicomweb
// NOTE: DCM4CHEE seems to return the data zipped
// NOTE: Orthanc returns the data with multi-part mime which cornerstoneWADOImageLoader doesn't
// know how to parse yet
//var uri = DICOMWeb.getString(instance['00081190']);
//uri = uri.replace('wado-rs', 'dicom-web');
// manually create a WADO-URI from the UIDs
// NOTE: Haven't been able to get Orthanc's WADO-URI to work yet - maybe its not configured?
var sopInstanceUid = remoteGetValue(instance['0008,0018']);
var uri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + "&contentType=application%2Fdicom";
// Add this instance to the current series
series.instances.push({
sopClassUid: remoteGetValue(instance['0008,0016']),
sopInstanceUid: sopInstanceUid,
uri: uri,
instanceNumber: parseFloat(remoteGetValue(instance['0020,0013']))
});
});
return seriesList;
}
/**
* Retrieve a set of instances using a QIDO call
* @param server
* @param studyInstanceUid
* @returns {{wadoUriRoot: String, studyInstanceUid: String, seriesList: Array}}
*/
Services.REMOTE.Instances = function(server, studyInstanceUid) {
var parameters = {
PatientName: "",
PatientID: "",
AccessionNumber: "",
SeriesInstanceUID: "",
SeriesNumber : "",
SOPClassUID : "",
InstanceNumber : ""
};
var remote = new OrthancRemote(server.root, server.sourceAE);
return {
wadoUriRoot: server.wadoUriRoot,
studyInstanceUid: studyInstanceUid,
seriesList: resultDataToStudyMetadata(server, studyInstanceUid, remote.findInstances(server.modality, studyInstanceUid, null, parameters))
};
};
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/**
* Parses the SourceImageSequence, if it exists, in order
* to return a ReferenceSOPInstanceUID. The ReferenceSOPInstanceUID
* is used to refer to this image in any accompanying DICOM-SR documents.
*
* @param instance
* @returns {String} The ReferenceSOPInstanceUID
*/
function getSourceImageInstanceUid(instance) {
// TODO= Parse the whole Source Image Sequence
// This is a really poor workaround for now.
// Later we should probably parse the whole sequence.
var SourceImageSequence = remoteGetValue(instance['0008,2112']);
if (SourceImageSequence && SourceImageSequence.Value && SourceImageSequence.Value.length) {
return SourceImageSequence.Value[0]['0008,1155'].Value[0];
}
}
/**
* Parses result data from a WADO search into Study MetaData
* Returns an object populated with study metadata, including the
* series list.
*
* @param server
* @param studyInstanceUid
* @param resultData
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
*/
function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
var seriesMap = {};
var seriesList = [];
if (!resultData.length) {
return;
}
var anInstance = resultData[0];
if (!anInstance) {
return;
}
var studyData = {
seriesList: seriesList,
patientName: remoteGetValue(anInstance['0010,0010']),
patientId: remoteGetValue(anInstance['0010,0020']),
accessionNumber: remoteGetValue(anInstance['0008,0050']),
studyDate: remoteGetValue(anInstance['0008,0020']),
modalities: remoteGetValue(anInstance['0008,0061']),
studyDescription: remoteGetValue(anInstance['0008,1030']),
imageCount: remoteGetValue(anInstance['0020,1208']),
studyInstanceUid: remoteGetValue(anInstance['0020,000d'])
};
resultData.forEach(function(instance) {
var seriesInstanceUid = remoteGetValue(instance['0020,000e']);
var series = seriesMap[seriesInstanceUid];
if (!series) {
series = {
seriesDescription: remoteGetValue(instance['0008,103e']),
modality: remoteGetValue(instance['0008,0060']),
seriesInstanceUid: seriesInstanceUid,
seriesNumber: parseFloat(remoteGetValue(instance['0020,0011'])),
instances: []
};
seriesMap[seriesInstanceUid] = series;
seriesList.push(series);
}
var sopInstanceUid = remoteGetValue(instance['0008,0018']);
var instanceSummary = {
imageType: remoteGetValue(instance['0008,0008']),
sopClassUid: remoteGetValue(instance['0008,0016']),
sopInstanceUid: sopInstanceUid,
instanceNumber: parseFloat(remoteGetValue(instance['0020,0013'])),
imagePositionPatient: remoteGetValue(instance['0020,0032']),
imageOrientationPatient: remoteGetValue(instance['0020,0037']),
frameOfReferenceUID: remoteGetValue(instance['0020,0052']),
sliceLocation: parseFloat(remoteGetValue(instance['0020,1041'])),
samplesPerPixel: parseFloat(remoteGetValue(instance['0028,0002'])),
photometricInterpretation: remoteGetValue(instance['0028,0004']),
rows: parseFloat(remoteGetValue(instance['0028,0010'])),
columns: parseFloat(remoteGetValue(instance['0028,0011'])),
pixelSpacing: remoteGetValue(instance['0028,0030']),
bitsAllocated: parseFloat(remoteGetValue(instance['0028,0100'])),
bitsStored: parseFloat(remoteGetValue(instance['0028,0101'])),
highBit: parseFloat(remoteGetValue(instance['0028,0102'])),
pixelRepresentation: parseFloat(remoteGetValue(instance['0028,0103'])),
windowCenter: remoteGetValue(instance['0028,1050']),
windowWidth: remoteGetValue(instance['0028,1051']),
rescaleIntercept: parseFloat(remoteGetValue(instance['0028,1052'])),
rescaleSlope: parseFloat(remoteGetValue(instance['0028,1053'])),
sourceImageInstanceUid: getSourceImageInstanceUid(instance),
laterality: remoteGetValue(instance['0020,0062']),
viewPosition: remoteGetValue(instance['0018,5101']),
numFrames: parseFloat(remoteGetValue(instance['0028,0008'])),
frameTime: parseFloat(remoteGetValue(instance['0018,1063']))
};
var iid = instance['xxxx,0001'].Value;
if (server.imageRendering === 'wadouri') {
instanceSummary.wadouri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + "&contentType=application%2Fdicom";
} else if (server.imageRendering == 'orthanc') {
instanceSummary.wadouri = server.root + '/instances/' + iid + '/file';
} else {
instanceSummary.wadorsuri = server.wadoRoot + '/studies/' + studyInstanceUid + '/series/' + seriesInstanceUid + '/instances/' + sopInstanceUid + '/frames/1';
}
series.instances.push(instanceSummary);
});
console.log(studyData.seriesList[0].instances);
return studyData;
}
/**
* Retrieved Study MetaData from a DICOM server using a WADO call
* @param server
* @param studyInstanceUid
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
*/
Services.REMOTE.RetrieveMetadata = function(server, studyInstanceUid) {
var remote = new OrthancRemote(server.root, server.sourceAE);
var study = resultDataToStudyMetadata(server, studyInstanceUid, remote.retrieveMetadata(server.modality, studyInstanceUid));
if (!study) {
study = {};
}
study.wadoUriRoot = server.wadoUriRoot;
study.studyInstanceUid = studyInstanceUid;
return study;
};
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function resultDataToStudies(resultData) {
var studies = [];
resultData.forEach(function(study) {
studies.push({
studyInstanceUid: remoteGetValue(study['0020,000d']),
// 00080005 = SpecificCharacterSet
studyDate: remoteGetValue(study['0008,0020']),
studyTime: remoteGetValue(study['0008,0030']),
accessionNumber: remoteGetValue(study['0008,0050']),
referringPhysicianName: remoteGetValue(study['0008,0090']),
// 00081190 = URL
patientName: remoteGetValue(study['0010,0010']),
patientId: remoteGetValue(study['0010,0020']),
patientBirthdate: remoteGetValue(study['0010,0030']),
patientSex: remoteGetValue(study['0010,0040']),
studyId: remoteGetValue(study['0020,0010']),
numberOfStudyRelatedSeries: parseFloat(remoteGetValue(study['0020,1206'])),
numberOfStudyRelatedInstances: parseFloat(remoteGetValue(study['0020,1208'])),
studyDescription: remoteGetValue(study['0008,1030']),
modalities: remoteGetValue(study['0008,0061'])
});
});
return studies;
}
Services.REMOTE.Studies = function(server, filter) {
var parameters = {
PatientName: filter.patientName ? filter.patientName : "",
PatientID: filter.patientId,
AccessionNumber: filter.accessionNumber ? filter.accessionNumber : "",
StudyDescription: "",
StudyDate : "",
StudyTime : "",
ReferringPhysicianName : "",
PatientBirthDate : "",
PatientSex : "",
StudyID : "",
NumberOfStudyRelatedSeries : "",
NumberOfStudyRelatedInstances : "",
ModalitiesInStudy : ""
};
var remote = new OrthancRemote(server.root, server.sourceAE);
var data = remote.findStudies(server.modality, parameters);
return resultDataToStudies(data.results);
};
@@ -0,0 +1,144 @@
/**
* Creates a URL for a WADO search
*
* @param server
* @param studyInstanceUid
* @returns {string}
*/
function buildUrl(server, studyInstanceUid) {
return server.wadoRoot + '/studies/' + studyInstanceUid + '/metadata';
}
/**
* Parses the SourceImageSequence, if it exists, in order
* to return a ReferenceSOPInstanceUID. The ReferenceSOPInstanceUID
* is used to refer to this image in any accompanying DICOM-SR documents.
*
* @param instance
* @returns {String} The ReferenceSOPInstanceUID
*/
function getSourceImageInstanceUid(instance) {
// TODO= Parse the whole Source Image Sequence
// This is a really poor workaround for now.
// Later we should probably parse the whole sequence.
var SourceImageSequence = instance['00082112'];
if (SourceImageSequence && SourceImageSequence.Value && SourceImageSequence.Value.length) {
return SourceImageSequence.Value[0]['00081155'].Value[0];
}
}
/**
* Parses result data from a WADO search into Study MetaData
* Returns an object populated with study metadata, including the
* series list.
*
* @param server
* @param studyInstanceUid
* @param resultData
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
*/
function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
var seriesMap = {};
var seriesList = [];
if (!resultData.length) {
return;
}
var anInstance = resultData[0];
if (!anInstance) {
return;
}
var studyData = {
seriesList: seriesList,
patientName: DICOMWeb.getName(anInstance['00100010']),
patientId: DICOMWeb.getString(anInstance['00100020']),
accessionNumber: DICOMWeb.getString(anInstance['00080050']),
studyDate: DICOMWeb.getString(anInstance['00080020']),
modalities: DICOMWeb.getString(anInstance['00080061']),
studyDescription: DICOMWeb.getString(anInstance['00081030']),
imageCount: DICOMWeb.getString(anInstance['00201208']),
studyInstanceUid: DICOMWeb.getString(anInstance['0020000D'])
};
resultData.forEach(function(instance) {
var seriesInstanceUid = DICOMWeb.getString(instance['0020000E']);
var series = seriesMap[seriesInstanceUid];
if (!series) {
series = {
seriesDescription: DICOMWeb.getString(instance['0008103E']),
modality: DICOMWeb.getString(instance['00080060']),
seriesInstanceUid: seriesInstanceUid,
seriesNumber: DICOMWeb.getNumber(instance['00200011']),
instances: []
};
seriesMap[seriesInstanceUid] = series;
seriesList.push(series);
}
var sopInstanceUid = DICOMWeb.getString(instance['00080018']);
var instanceSummary = {
imageType: DICOMWeb.getString(instance['00080008']),
sopClassUid: DICOMWeb.getString(instance['00080016']),
sopInstanceUid: sopInstanceUid,
instanceNumber: DICOMWeb.getNumber(instance['00200013']),
imagePositionPatient: DICOMWeb.getString(instance['00200032']),
imageOrientationPatient: DICOMWeb.getString(instance['00200037']),
frameOfReferenceUID: DICOMWeb.getString(instance['00200052']),
sliceLocation: DICOMWeb.getNumber(instance['00201041']),
samplesPerPixel: DICOMWeb.getNumber(instance['00280002']),
photometricInterpretation: DICOMWeb.getString(instance['00280004']),
rows: DICOMWeb.getNumber(instance['00280010']),
columns: DICOMWeb.getNumber(instance['00280011']),
pixelSpacing: DICOMWeb.getString(instance['00280030']),
bitsAllocated: DICOMWeb.getNumber(instance['00280100']),
bitsStored: DICOMWeb.getNumber(instance['00280101']),
highBit: DICOMWeb.getNumber(instance['00280102']),
pixelRepresentation: DICOMWeb.getNumber(instance['00280103']),
windowCenter: DICOMWeb.getString(instance['00281050']),
windowWidth: DICOMWeb.getString(instance['00281051']),
rescaleIntercept: DICOMWeb.getNumber(instance['00281052']),
rescaleSlope: DICOMWeb.getNumber(instance['00281053']),
sourceImageInstanceUid: getSourceImageInstanceUid(instance),
laterality: DICOMWeb.getString(instance['00200062']),
viewPosition: DICOMWeb.getString(instance['00185101']),
numFrames: DICOMWeb.getNumber(instance['00280008']),
frameTime: DICOMWeb.getNumber(instance['00181063']),
sliceThickness: DICOMWeb.getNumber(instance['00180050'])
};
if (server.imageRendering === 'wadouri') {
instanceSummary.wadouri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + '&contentType=application%2Fdicom';
} else {
instanceSummary.wadorsuri = server.wadoRoot + '/studies/' + studyInstanceUid + '/series/' + seriesInstanceUid + '/instances/' + sopInstanceUid + '/frames/1';
}
series.instances.push(instanceSummary);
});
return studyData;
}
/**
* Retrieved Study MetaData from a DICOM server using a WADO call
* @param server
* @param studyInstanceUid
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
*/
Services.WADO.RetrieveMetadata = function(server, studyInstanceUid) {
var url = buildUrl(server, studyInstanceUid);
var result = DICOMWeb.getJSON(url, server.requestOptions);
var study = resultDataToStudyMetadata(server, studyInstanceUid, result.data);
if (!study) {
study = {};
}
study.wadoUriRoot = server.wadoUriRoot;
study.studyInstanceUid = studyInstanceUid;
return study;
};